T-junction is a classical structure for the two-phase separation. The analysis of gas-liquid flow and the interface movement at the T-junction is very important to the mechanism understanding especially for T-micro-junctions with unequal diameter joint. A simulation of the passive draining process and the corresponding flow pattern modulation of slug flow in a tube with three T-micro-junctions are presented in this paper. Using the volume of fluid (VOF) method and the dynamic grid adaption method the interface movement was tracked precisely especially at the region of drainage junctions. As results, with the separation of liquid no apparent change of gas slugs’ length but shortened water plugs. The gas fraction in main tube is increased more than 10%. During the separation process, the interface movement at unequal diameter junctions mainly consisted of three stages: the generation of penetrating bubbles, a stable sliding stage and the retraction to mother bubble. These constitute one piston movement of penetrating bubbles, which is the vital mechanism of phase separation. The cooperation of interface pressure difference, surface tension, interphase shear force and characteristic sizes of micro-channel drainages brings into a separation. A preliminary model to optimize characteristic sizes of porous materials is proposed in order to getting a successful liquid separation from a slug flow, which could improve the condensation heat transfer performance.